This project involves analysis of structure-function relationships in the enzymes of the mandelate pathway in P. putida and enzymes that are structurally homologous from other metabolic pathways. We have recently published several papers describing structure-function relationships in the enolase superfamily, the superfamily to which mandelate race belongs. These homologous proteins perform different overall functions using a range of different substrates. The common structures reflect a common fundamental chemical step that these enzymes all perform and provides a model system for studying how nature has conscripted the common architecture for a range of metabolic functions. The Computer Graphics Laboratory is essential to further development of this work: using models of the known homologs to design more general models of the scaffold are useful in helping us to understand how differences in sequence generate differences in function. This work seeks to utilize comparative study of homologous enzyme structures to learn more about general principles useful in re-engineering proteins. We use MidasPlus software and pre-release versions of new software that will appear in Chimera to develop new computational approaches for these studies.